<p>Here, we seek to address the importance of biodiversity in plant ecosystems. We examined the productivity-diversity relationship through the lens of the modern coexistence theory, using a combination of both experimentation and mathematical simulation. We did this by tracking and comparing the productivity of mixed and monoculture plots, analyzing the growth responses of individual trees at forest plots (Chapter 1), confirming the productivity-diversity relationship in a greenhouse experiment using local herbaceous plants (Chapter 2), and finally simulating the productivity response of monoculture vs polyculture plantations to specialist enemy attack (Chapter 3).</p><p>It is no surprise that biodiversity has been decreasing at an exponential rate on the global scale because of effects such as habitat fragmentation, invasive species, spreading pathogens, and anthropogenic influences. Ecologists often found that plants in more species rich locations often exhibited higher productivity and stability in the face of stress. One such phenomenon is known as the productivity diversity relationship that implies biodiversity is key to sustaining ecosystems. Notably, while efforts are being put forth to address ecosystem destruction, much of the current tree planting strategy in the USA is based on timber profit rather than forest productivity and species coexistence with tree biology often being a secondary consideration. These thought processes are in opposition with historical experiments that indicate polyculture communities create more biomass making them significantly more productive than monocultures. However, we also acknowledge that it is not simply biodiversity that must be taken into consideration for a productive ecosystem but also species interaction through coexistence indicate whether or not a community will persevere. These interactions can be addressed using the modern coexistence theory which depends on these complementarity and fitness similarities for species to coexist through time. Here, we seek to address the importance of biodiversity in plant ecosystems. We examined the productivity-diversity relationship through the lens of the modern coexistence theory, using a combination of both experimentation and mathematical simulation. We did this by tracking and comparing the productivity of mixed and monoculture plots, analyzing the growth responses of individual trees at forest plots (Chapter 1), confirming the productivity-diversity relationship in a greenhouse experiment using local herbaceous plants (Chapter 2), and finally simulating the productivity response of monoculture vs polyculture plantations to specialist enemy attack (Chapter 3). Our research across the combination of approaches used found that species with overlapping niches and very different finesses will exclude one another due to high competition. Further, the productivity diversity correlation is necessary for ecosystem growth, but it is not sufficient for species coexistence. However, species can maintain this positive relationship despite a lack of coexistence if they maintain niche complementarity. Lastly, using a theoretic game model we were able to identify the impacts of a specialist pest on polyculture and monoculture forest. These results showed that a polyculture forest was more productive than that of a monoculture forest regardless of the presence of a specialist enemy. The results of the multiple threads of evidence found from these combined experiments indicate that while the productivity diversity correlation is important to ecosystems it is likely due to the impacts of niche complementarity that determine whether or not species will be productive within an ecosystem.</p>

<p dir="ltr">To examine how forest management affects terrestrial salamanders, this dissertation: (1) examines the effects of timber harvesting strategies on salamanders; (2) examines the effects of prescribed fire for oak regeneration on salamander populations; and (3) explores the influence of artificial cover object (ACO) wood type, size and shape, and placement on salamander monitoring results. These projects were conducted at the Hardwood Ecosystem Experiment (HEE) and Martell Experimental Forest in Indiana. Long-term salamander monitoring data from the HEE were used to examine the effects of clearcuts, shelterwoods, and patch cuts on salamander captures collected up to eleven years post-harvest and were analyzed with a before-after-control-impact (BACI) design. Clearcuts and patch cuts had negative effects on salamanders 4-6 years post-harvest, which coincided with a drought; however, preparatory and establishment shelterwood harvests showed no effects on salamander captures, suggesting that retaining canopy cover may protect salamanders from compound disturbances such as drought. Also at the HEE, capture-recapture techniques were used to examine salamander population estimates before and after fire. Only two of three fires affected salamander populations. In the short term, prescribed fire effects on salamanders may be weak and intermittent and microclimate may have a greater effect on populations, although the longer-term effects of fire remain unknown. At Martell Experimental Forest, salamander numbers were compared beneath ACOs of different wood types, sizes and shapes, and grid arrays of different spacings. Pine ACOs were preferred over ash, while several small ACOs yielded equal salamander numbers to one large ACO of equal total area. High ACO density may increase capture probability but reduce the area sampled by each ACO, while lower density ACO grids may cover a larger area with the same sampling effort and produce more comparable results, but with less precision; choice of ACO experimental design will therefore require careful consideration of management goals. This dissertation also suggests strategies to support salamander populations as guidelines for managers to consider in management planning.</p>

<p dir="ltr">Non-native biological invasions are one of the leading concerns for global biodiversity. The establishment of invasive species reduces local biodiversity, shifts species composition, changes successional trajectories, and alters ecosystem functions. This thesis examines two aspects of invasive plants: (1) the distribution and the most important climatic and anthropogenic drivers of invasive trees across the eastern United States, and (2) an evaluation of invasive plant removal and herbaceous recovery from a government cost-share program that provides financial support for invasive plant management by private landowners.</p><p><br></p><p dir="ltr">Our first study focused on identifying the distribution of invasive trees, and the factors associated with their distribution. This is essential to predicting spread and planning subsequent management. Using USDA Forest Inventory Analysis (FIA) data and random forest modeling, we examined the distribution, and variables associated with the distribution, of invasive tree species. Invasive trees were found in 10,511 out of 299,387 FIA plots. Invasive species basal area and density (trees per ha; TPH) were highest within the central and southern Appalachian Mountains, Michigan, the Northeast, and the southern Coastal Plain of the United States. A random forest model of invasive species basal area (R²= 0.47, RMSE = 0.47) and density (R²=0.46, RMSE=0.50) vs. environmental variables found that both invasive basal area and density were most strongly associated with human footprint, followed by various climatic variables. An equivalent model of native tree basal (R²=0.53, RMSE=9.25) and TPH (R²=0.47, RMSE=8.64) found that native tree basal area and density were most strongly associated with aridity followed by various climatic variables. As human footprint increased, invasive tree basal area and density increased. These results suggest that the distribution of invasive trees is reliant on human alterations to forests.</p><p><br></p><p dir="ltr">Our second study focused on Environmental Quality Incentives Program (EQIP), a federal cost-share program that has provided $25 billion of financial assistance to farmers and non-industrial private forest owners. Few studies have examined whether this program facilitates the recovery of the herbaceous layer while decreasing the dominance of invasive plant species. We surveyed the herbaceous layer of EQIP-treated and untreated (reference) forests across three physiographic regions of Indiana. Using non-metric multidimensional scaling (NMDS) ordination and linear mixed effects models, we evaluated the species composition, richness, diversity, evenness, floristic quality index, and herbaceous-layer cover of EQIP and reference sites. We also used linear mixed models to evaluate how EQIP site treatment affected the diversity of native plant species. Sites treated with EQIP contracts typically had significantly higher native species richness, Shannon’s diversity, and floristic quality than reference sites. There were significant separations in species composition between EQIP treated and reference forests state-wide and in the southern non-glaciated region of Indiana, although composition overlapped between EQIP and reference forests. Our study suggests that EQIP-funded treatments promote increased species richness and diversity. However, the persistent overlap in species composition we observed may signify biotic homogenization due to a long-shared history of anthropogenic disturbances between EQIP and reference sites. Therefore, active restoration of the herbaceous layer might be needed to allow a full recovery after invasive removal.</p>

<p dir="ltr">To reduce the establishment and spread of invasive plant species, the Environmental Quality Incentive Program (EQIP) was created in 1996 to provide financial and technical assistance to private landowners to aid in conservation practices and address environmental concerns. From 2014-2022, approximately $90 million dollars was obligated to the EQIP for completed contracts of over 240,000 hectares in Indiana. However, to date, there has been no examination of whether participation in conversation cost sharing programs has resulted in the recovery of native tree diversity, growth, and reproduction following the treatment of invasive plants. Furthermore, there is a gap in our understanding of the effectiveness of EQIP and its success in achieving and maintaining management goals. This thesis quantifies the composition, diversity, regeneration density and growth of tree species in response to invasive plant treatments at sites that participated in the EQIP. In particular, I investigated how the species composition of woody seedlings (stems < 2 cm dbh) and woody saplings (2 – 5 cm dbh) differed across EQIP-treated and untreated reference plots. I then examined how native species richness and diversity values differed between EQIP-treated and untreated plots. Lastly, I used dendroecological methods to determine how treatment of invasive shrubs affected overstory tree growth. Across the state, I found that native species richness of seedlings and saplings was greater in EQIP-treated plots then within reference plots. Reference plots were associated with invasive species such as <i>Lonicera maackii</i> (Amur honeysuckle), <i>Rosa multiflora</i> (multiflora rose), <i>Elaeagnus umbellata</i> (autumn olive) and <i>L. japonica</i> (Japanese honeysuckle), while EQIP-treated plots were associated with native tree species, such as <i>Carya ovata</i> (shagbark hickory),<i> Ulmus americana </i>(American elm), <i>Fraxinus americana</i> (white ash), <i>Liriodendron tulipifera</i> (yellow-poplar), <i>Quercus alba</i> (white oak), <i>Q. velutina</i> (black oak), and shrubs, such as <i>Rubus allegheniensis</i> (Allegheny blackberry) and <i>Lindera benzoin</i> (spicebush). I observed that trees generally had greater basal area increment growth following invasive shrub treatments; therefore, the reduction of invasive shrub dominance on EQIP-enrolled lands has led to a small, but significant, increase in overstory tree growth. I observed high within-group variability in growth for EQIP-treated and reference plots, likely due to differing management strategies across privately owned forests. Overall, my results demonstrate that participation in the EQIP has positively benefited species richness, and native species composition, and tree growth.</p>

<div>Anthropogenically driven global change is disrupting ecosystems and habitats of many plant species, straining the ability of native species to survive and reproduce. The overarching goal of this research was to holistically work towards restoration of a threatened tree species by connecting research from different disciplines. In order to do so, the threatened butternut tree (<i>Juglans cinerea</i>) and its hybrids were used as a case study. Hybridization can incorporate stress tolerance in plants and could be a potential restoration tool. Evidence in some wild butternut populations indicates that naturalized hybrids of butternut with Japanese walnut (<i>Juglans ailantifolia</i>) may be more tolerant to butternut canker disease (BCD) than butternut, but this has not been formally tested. Thus, chapter 2 examined potential BCD tolerance within and between unadmixed and hybrid butternut inoculated with two BCD fungal isolates. Differences in canker growth were observed by fungal isolate, which could help to explain some differences in BCD severity found among butternut populations. Smaller and fewer cankers and greater genetic gains were detected in hybrid families, demonstrating that hybrids warrant further evaluation as a possible breeding tool for developing BCD-resistant butternut trees.</div><div>However, even with increased disease tolerance, hybrids must possess similar ecophysiological tolerances to their native progenitor to be an effective replacement. Butternut is extremely cold hardy, but Japanese walnuts are native to a warmer ecosystem, indicating potential disparities in extreme temperature tolerances between the two species and their hybrids. Thus, samples from mature trees were subjected to cold and heat treatments to compare relative extreme temperature tolerances within butternut and between butternut, Japanese walnut, and their hybrids. Within butternut, trees from colder areas exhibited less cold damage than those from warmer areas. Differences in heat damage among provenances occurred but did not follow a clear trend. Butternut exhibited greatest cold tolerance, Japanese walnut exhibited greatest heat tolerance, and hybrids were intermediate. Thus, the utility of hybrids for restoration could be limited at the extremes of the species’ distributions.</div><div>A second, but different type of freeze test was conducted for chapter 4 using seedlings to gain a more nuanced understanding of cold tolerance within butternut and between butternut and its hybrids. No survival or damage differences were detected in butternut provenances, although seedlings from the coldest provenances experienced more delayed budbreak at the two warmest treatments than those from warmer provenances. Interspecific differences were not observed in dieback but were detected in survival and budbreak. The hybrids had greater survival than butternut from warmer provenances at the lowest temperature treatment (-38 °C), but given that temperatures that low are extremely unlikely to occur in those provenances, it is not anticipated to give the hybrids an advantage if planted in those areas. However, the hybrids’ earlier budbreak could limit the success of restoration with these hybrids in the coldest extents of butternut’s range. </div><div>If hybrids, as well as genetically modified (GM) trees, are successfully developed for effective disease tolerance and to serve as an ecologically suitable replacement, success of restoration using hybrids will ultimately depend on those directly responsible for replanting efforts. A survey was administered to land managers in 46 organizations in Indiana to gauge perceptions of hybrid and GM trees, as well as current use of hybrid trees. Land managers had stronger concern for ecological, rather than economic, issues. Agreement was highest for using hybrid and GM trees for “conservation and restoration of at-risk species”, “timber production”, and “non-timber products (fruit, syrup, etc.)”. However, perceptions varied by characteristics, such as concern type, age, and the type of land they managed. Ecological concern and the type of land being managed most strongly predicted current hybrid use. Overall, results indicate the majority of land managers in Indiana would likely be agreeable to recommendations towards using hybrids. However, most nonetheless had strong ecological concerns about their suitability as a native replacement. It is important to note, though, that consistent with the results of previous studies, great variation was seen within the performance and characteristics of the butternut hybrids in chapters 2-4. Thus, it may be possible with careful selection and breeding to harness this variation to develop disease tolerant and ecologically similar hybrids acceptable to land managers.</div>